API Documentation

Important

All properties exchanged with the xtb API are given in atomic units. For integrations with other frameworks the unit conventions might differ and require conversion.

Calculation Environment

class xtb.interface.Environment[source]

Wraps an API object representing a TEnvironment class in xtb. The API object is constructed automatically and deconstructed on garbage collection, it stores the IO configuration and the error log of the API.

All API calls require an environment object, usually this is done automatically as all other classes inherent from the calculation environment.

Example

>>> from xtb.libxtb import VERBOSITY_FULL
>>> from xtb.interface import Environment
>>> env = Environment()
>>> env.set_output("error.log")
>>> env.set_verbosity(VERBOSITY_FULL)
>>> if env.check != 0:
...     env.show("Error message")
...
>>> env.release_output()
check() → int[source]

Check current status of calculation environment

Example

>>> if env.check() != 0:
...     raise XTBException("Error occured in the API")
get_error(message: Optional[str] = None) → str[source]

Check for error messages

Example

>>> if env.check() != 0:
...     raise XTBException(env.get_error())
release_output() → None[source]

Release output unit from this environment

set_output(filename: str) → None[source]

Bind output from this environment

set_verbosity(verbosity: int) → None[source]

Set verbosity of calculation output

show(message: str) → None[source]

Show and empty error stack

Molecular Structure Data

class xtb.interface.Molecule(numbers: numpy.ndarray, positions: numpy.ndarray, charge: Optional[float] = None, uhf: Optional[int] = None, lattice: Optional[numpy.ndarray] = None, periodic: Optional[numpy.ndarray] = None)[source]

Represents a wrapped TMolecule API object in xtb. The molecular structure data object has a fixed number of atoms and immutable atomic identifiers.

Example

>>> from xtb.interface import Molecule
>>> import numpy as np
>>> numbers = np.array([8, 1, 1])
>>> positions = np.array([
... [ 0.00000000000000, 0.00000000000000,-0.73578586109551],
... [ 1.44183152868459, 0.00000000000000, 0.36789293054775],
... [-1.44183152868459, 0.00000000000000, 0.36789293054775]])
...
>>> mol = Molecule(numbers, positions)
>>> len(mol)
3
>>> mol.update(np.zeros((len(mol), 3)))  # will fail nuclear fusion check
xtb.interface.XTBException: Update of molecular structure failed:
-1- xtb_api_updateMolecule: Could not update molecular structure
>>> mol.update(positions)
Raises:
  • ValueError – on invalid input on the Python side of the API
  • XTBException – on errors returned from the API
update(positions: numpy.ndarray, lattice: Optional[numpy.ndarray] = None) → None[source]

Update coordinates and lattice parameters, both provided in atomic units (Bohr). The lattice update is optional also for periodic structures.

Generally, only the cartesian coordinates and the lattice parameters can be updated, every other modification, regarding total charge, total spin, boundary condition, atomic types or number of atoms requires the complete reconstruction of the object.

Raises:
  • ValueError – on invalid input on the Python side of the API
  • XTBException – on errors returned from the API, usually from nuclear fusion check

Single Point Calculator

class xtb.interface.Calculator(param: xtb.interface.Param, numbers: List[int], positions: List[float], charge: Optional[float] = None, uhf: Optional[int] = None, lattice: Optional[List[float]] = None, periodic: Optional[List[bool]] = None)[source]

This calculator represents a calculator object in the xtb API and provides access to all methods implemented with a unified interface. The API object must be loaded with a parametrisation before it can be used in any other API request.

The parametrisation loading is included in the initialization in this class, which has the advantage that all API functionality is readily available, the downside is that a calculator object on the Python side can only carry one distinct parametrisation, which is not allowed to change.

Examples

>>> from xtb.libxtb import VERBOSITY_MINIMAL
>>> from xtb.interface import Calculator, Param
>>> import numpy as np
>>> numbers = np.array([8, 1, 1])
>>> positions = np.array([
... [ 0.00000000000000, 0.00000000000000,-0.73578586109551],
... [ 1.44183152868459, 0.00000000000000, 0.36789293054775],
... [-1.44183152868459, 0.00000000000000, 0.36789293054775]])
...
>>> calc = Calculator(Param.GFN2xTB, numbers, positions)
>>> calc.set_verbosity(VERBOSITY_MINIMAL)
>>> res = calc.singlepoint()  # energy printed is only the electronic part
   1     -5.1027888 -0.510279E+01  0.421E+00   14.83       0.0  T
   2     -5.1040645 -0.127572E-02  0.242E+00   14.55       1.0  T
   3     -5.1042978 -0.233350E-03  0.381E-01   14.33       1.0  T
   4     -5.1043581 -0.602769E-04  0.885E-02   14.48       1.0  T
   5     -5.1043609 -0.280751E-05  0.566E-02   14.43       1.0  T
   6     -5.1043628 -0.188160E-05  0.131E-03   14.45      44.1  T
   7     -5.1043628 -0.455326E-09  0.978E-04   14.45      59.1  T
   8     -5.1043628 -0.572169E-09  0.192E-05   14.45    3009.1  T
     SCC iter.                  ...        0 min,  0.022 sec
     gradient                   ...        0 min,  0.000 sec
>>> res.get_energy()
-5.070451354836705
>>> res.get_gradient()
[[ 6.24500451e-17 -3.47909735e-17 -5.07156941e-03]
 [-1.24839222e-03  2.43536791e-17  2.53578470e-03]
 [ 1.24839222e-03  1.04372944e-17  2.53578470e-03]]
Raises:XTBException – on errors encountered in API or while performing calculations
release_external_charges() → None[source]

Unset external point charge field

set_accuracy(accuracy: float) → None[source]

Set numerical accuracy for calculation, ranges from 1000 to 0.0001, values outside this range will be cutted with warning placed in the error log, which can be retrieved by get_error() but will not trigger check().

Example

>>> calc.set_accuracy(1.0)
set_electronic_temperature(etemp: int) → None[source]

Set electronic temperature in K for tight binding Hamiltonians, values smaller or equal to zero will be silently ignored by the API.

Example

>>> calc.set_electronic_temperature(300.0)
set_external_charges(numbers: numpy.ndarray, charges: numpy.ndarray, positions: numpy.ndarray) → None[source]

Set an external point charge field

set_max_iterations(maxiter: int) → None[source]

Set maximum number of iterations for self-consistent charge methods, values smaller than one will be silently ignored by the API. Failing to converge in a given number of cycles is not necessarily reported as an error by the API.

Example

>>> calc.set_max_iterations(100)
set_solvent(solvent: Optional[xtb.interface.Solvent] = None) → None[source]

Add/Remove a solvation model to/from calculator

Example

>>> from xtb.utils import get_solvent, Solvent
...
>>> calc.set_solvent(Solvent.h2o)  # Set solvent to water with enumerator
>>> calc.set_solvent()  # Release solvent again
>>> calc.set_solvent(get_solvent("CHCl3"))  # Find correct enumerator
singlepoint(res: Optional[xtb.interface.Results] = None, copy: bool = False) → xtb.interface.Results[source]

Perform singlepoint calculation, note that the a previous result is overwritten by default.

Example

>>> res = calc.singlepoint()
>>> res = calc.singlepoint(res)
>>> calc.singlepoint(res)  # equivalent to the above
>>> new = calc.singlepoint(res, copy=True)

Calculation Results

class xtb.interface.Results(res: Union[xtb.interface.Molecule, Results])[source]

Holds xtb API object containing results from a single point calculation. It can be queried for indiviual properties or used to restart calculations. Note that results from different methods are generally incompatible, the API tries to be as clever as possible about this and will usually automatically reallocate missmatched results objects as necessary.

The results objects is connected to its own, independent environment, giving it its own error stack and IO infrastructure.

Example

>>> from xtb.libxtb import VERBOSITY_MINIMAL
>>> from xtb.interface import Calculator, Param
>>> import numpy as np
>>> numbers = np.array([8, 1, 1])
>>> positions = np.array([
... [ 0.00000000000000, 0.00000000000000,-0.73578586109551],
... [ 1.44183152868459, 0.00000000000000, 0.36789293054775],
... [-1.44183152868459, 0.00000000000000, 0.36789293054775]])
...
>>> calc = Calculator(Param.GFN2xTB, numbers, positions)
>>> calc.set_verbosity(VERBOSITY_MINIMAL)
>>> res = calc.singlepoint()  # energy printed is only the electronic part
   1     -5.1027888 -0.510279E+01  0.421E+00   14.83       0.0  T
   2     -5.1040645 -0.127572E-02  0.242E+00   14.55       1.0  T
   3     -5.1042978 -0.233350E-03  0.381E-01   14.33       1.0  T
   4     -5.1043581 -0.602769E-04  0.885E-02   14.48       1.0  T
   5     -5.1043609 -0.280751E-05  0.566E-02   14.43       1.0  T
   6     -5.1043628 -0.188160E-05  0.131E-03   14.45      44.1  T
   7     -5.1043628 -0.455326E-09  0.978E-04   14.45      59.1  T
   8     -5.1043628 -0.572169E-09  0.192E-05   14.45    3009.1  T
     SCC iter.                  ...        0 min,  0.022 sec
     gradient                   ...        0 min,  0.000 sec
>>> res.get_energy()
-5.070451354836705
>>> res.get_gradient()
[[ 6.24500451e-17 -3.47909735e-17 -5.07156941e-03]
 [-1.24839222e-03  2.43536791e-17  2.53578470e-03]
 [ 1.24839222e-03  1.04372944e-17  2.53578470e-03]]
>>> res = calc.singlepoint(res)
   1     -5.1043628 -0.510436E+01  0.898E-08   14.45       0.0  T
   2     -5.1043628 -0.266454E-14  0.436E-08   14.45  100000.0  T
   3     -5.1043628  0.177636E-14  0.137E-08   14.45  100000.0  T
     SCC iter.                  ...        0 min,  0.001 sec
     gradient                   ...        0 min,  0.000 sec
>>> res.get_charges()
[-0.56317912  0.28158956  0.28158956]
Raises:XTBException – in case the requested property is not present in the results object
get_bond_orders() → numpy.ndarray[source]

Query singlepoint results object for bond orders

Example

>>> res.get_bond_orders()
[[0.00000000e+00 9.20433501e-01 9.20433501e-01]
 [9.20433501e-01 0.00000000e+00 2.74039053e-04]
 [9.20433501e-01 2.74039053e-04 0.00000000e+00]]
get_charges() → numpy.ndarray[source]

Query singlepoint results object for partial charges in e

Example

>>> get_charges()
[-0.56317913  0.28158957  0.28158957]
get_dipole() → numpy.ndarray[source]

Query singlepoint results object for dipole in e·Bohr

Example

>>> get_dipole()
[-4.44089210e-16  1.44419023e-16  8.89047667e-01]
get_energy() → float[source]

Query singlepoint results object for energy in Hartree

Example

>>> res.get_energy()
-5.070451354836705
get_gradient() → numpy.ndarray[source]

Query singlepoint results object for gradient in Hartree/Bohr

Example

>>> res.get_gradient()
[[ 6.24500451e-17 -3.47909735e-17 -5.07156941e-03]
 [-1.24839222e-03  2.43536791e-17  2.53578470e-03]
 [ 1.24839222e-03  1.04372944e-17  2.53578470e-03]]
get_number_of_orbitals() → int[source]

Query singlepoint results object for the number of basis functions

Example

>>> res.get_number_of_orbitals()
6
get_orbital_coefficients() → numpy.ndarray[source]

Query singlepoint results object for orbital coefficients

Example

>>> res.get_orbital_coefficients()
array([[-7.94626768e-01,  6.38378239e-16,  4.52990407e-01,
        -6.38746369e-16, -8.35495085e-01, -4.44089210e-16],
       [ 2.77555756e-17, -6.97332245e-01,  7.49400542e-16,
         1.88136491e-17,  7.21644966e-16, -9.60006511e-01],
       [ 2.17336312e-16, -1.08051945e-16, -1.11598977e-15,
        -1.00000000e+00,  5.74153329e-17,  3.30330107e-17],
       [-8.67578876e-02, -9.71445147e-16, -8.05763104e-01,
         7.71702239e-16, -7.18690020e-01, -4.71844785e-16],
       [-1.84540457e-01, -3.54572323e-01, -2.39090946e-01,
         2.87533552e-16,  7.68757806e-01,  9.02845514e-01],
       [-1.84540457e-01,  3.54572323e-01, -2.39090946e-01,
         2.01021058e-16,  7.68757806e-01, -9.02845514e-01]])
get_orbital_eigenvalues() → numpy.ndarray[source]

Query singlepoint results object for orbital energies in Hartree

Example

>>> res.get_orbital_eigenvalues()
array([-0.68087967, -0.56667693, -0.51373083, -0.44710101,  0.08394016,
        0.24142397])
get_orbital_occupations() → numpy.ndarray[source]

Query singlepoint results object for occupation numbers

Example

>>> res.get_orbital_occupations()
array([2., 2., 2., 2., 0., 0.])
get_virial() → numpy.ndarray[source]

Query singlepoint results object for virial given in Hartree

Example

>>> res.get_virial()
[[ 1.43012837e-02  3.43893209e-17 -1.86809511e-16]
 [ 0.00000000e+00  0.00000000e+00  0.00000000e+00]
 [ 1.02348685e-16  1.46994821e-17  3.82414977e-02]]

Available Calculation Methods

class xtb.interface.Param[source]

Possible parametrisations for the Calculator class

GFN0xTB = 3

Experimental non-self-consistent extended tight binding Hamiltonian using classical electronegativity equilibration electrostatics and extended Hückel Hamiltonian.

Geometry, frequency and non-covalent interactions parametrisation for elements up to Z=86.

Requires the param_gfn0-xtb.txt parameter file in the XTBPATH environment variable to load!

See: P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. DOI: 10.26434/chemrxiv.8326202.v1

GFN1xTB = 2

Self-consistent extended tight binding Hamiltonian with isotropic second order electrostatic contributions and third order on-site contributions.

Geometry, frequency and non-covalent interactions parametrisation for elements up to Z=86.

Cite as: S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118

GFN2xTB = 1

Self-consistent extended tight binding Hamiltonian with anisotropic second order electrostatic contributions, third order on-site contributions and self-consistent D4 dispersion.

Geometry, frequency and non-covalent interactions parametrisation for elements up to Z=86.

Cite as: C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176

GFNFF = 4

General force field parametrized for geometry, frequency and non-covalent interactions up to Z=86.

xtb API support is currently experimental.

Cite as: S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665–15673. DOI: 10.1002/anie.202004239

IPEAxTB = 5

Special parametrisation for the GFN1-xTB Hamiltonian to improve the description of vertical ionisation potentials and electron affinities. Uses additional diffuse s-functions on light main group elements. Parametrised up to Z=86.

Cite as: V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. DOI: `10.1039/c7sc00601b <https://dx.doi.org/10.1039/c7sc00601b`_

utils.get_method() → Optional[xtb.interface.Param]

Return the correct parameter enumerator for a string input.

Example

>>> get_method('GFN2-xTB')
<Param.GFN2xTB: 1>
>>> get_method('gfn2xtb')
<Param.GFN2xTB: 1>
>>> get_method('GFN-xTB') is None
True
>>> get_method('GFN1-xTB') is None
False